Deputy Prime Minister Mark Brown says there are processes place to address their concerns.
His assurance came in response to concerns raised by Democratic Party MP Selina Napa, who told Parliament some landowners would prefer to negotiate their own agreement.
Brown said there were legal avenues to resolve any disputes; that was a matter for officials.
The government and the landowners have previously disputed access to land for the pipeline project to deliver potable water to the people of Rarotonga.
But they have managed to work things out sufficiently to allow the $90 million project, which is nearing the completion of stage two, to proceed.